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- PDB-6fwv: The Bacillus anthracis TIE protein -

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Basic information

Entry
Database: PDB / ID: 6fwv
TitleThe Bacillus anthracis TIE protein
ComponentsCollagen Adhesion protein
KeywordsUNKNOWN FUNCTION / LPXTG-anchored / surface protein / thioester domain / isopeptide domain / TIE protein
Function / homology
Function and homology information


membrane => GO:0016020
Similarity search - Function
Uncharacterised domain CHP03934, TQXA / Thioester domain / Thioester domain / : / Prealbumin-like fold domain / Prealbumin-like fold domain / LPXTG cell wall anchor motif / Immunoglobulin-like fold
Similarity search - Domain/homology
Collagen Adhesion protein / Cell wall surface anchor family protein
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.58 Å
AuthorsMiller, O.K. / Banfield, M.J. / Schwarz-Linek, U.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/K001485 United Kingdom
Royal Society of Edinburgh United Kingdom
Citation
Journal: Protein Sci. / Year: 2018
Title: A new structural class of bacterial thioester domains reveals a slipknot topology.
Authors: Miller, O.K. / Banfield, M.J. / Schwarz-Linek, U.
#1: Journal: Elife / Year: 2015
Title: An internal thioester in a pathogen surface protein mediates covalent host binding.
Authors: Walden, M. / Edwards, J.M. / Dziewulska, A.M. / Bergmann, R. / Saalbach, G. / Kan, S.Y. / Miller, O.K. / Weckener, M. / Jackson, R.J. / Shirran, S.L. / Botting, C.H. / Florence, G.J. / ...Authors: Walden, M. / Edwards, J.M. / Dziewulska, A.M. / Bergmann, R. / Saalbach, G. / Kan, S.Y. / Miller, O.K. / Weckener, M. / Jackson, R.J. / Shirran, S.L. / Botting, C.H. / Florence, G.J. / Rohde, M. / Banfield, M.J. / Schwarz-Linek, U.
History
DepositionMar 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 21, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Revision 1.3Jun 5, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Collagen Adhesion protein
B: Collagen Adhesion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,2919
Polymers117,8332
Non-polymers4587
Water99155
1
A: Collagen Adhesion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1785
Polymers58,9161
Non-polymers2624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Collagen Adhesion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1134
Polymers58,9161
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)208.824, 66.500, 106.581
Angle α, β, γ (deg.)90.000, 116.810, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-721-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 4 - 525 / Label seq-ID: 4 - 525

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Collagen Adhesion protein


Mass: 58916.410 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: BASH2_00722 / Plasmid: pEHisTEV / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0F7RA58, UniProt: A0A6L8P957*PLUS
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 6000, sodium cacodylate, zinc acetate, methanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 2.58→93.18 Å / Num. obs: 40944 / % possible obs: 99 % / Redundancy: 3.7 % / Biso Wilson estimate: 77.11 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.064 / Net I/σ(I): 13.1
Reflection shellResolution: 2.58→2.65 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.778 / Mean I/σ(I) obs: 1.2 / CC1/2: 0.6 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMACrefinement
PDB_EXTRACT3.24data extraction
xia2data reduction
xia2data scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.58→93.18 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.918 / SU B: 32.342 / SU ML: 0.304 / SU R Cruickshank DPI: 0.6821 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.682 / ESU R Free: 0.31
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2556 2028 5 %RANDOM
Rwork0.2213 ---
obs0.2231 38916 98.81 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 238.55 Å2 / Biso mean: 77.111 Å2 / Biso min: 29.31 Å2
Baniso -1Baniso -2Baniso -3
1--2.47 Å20 Å2-1.77 Å2
2--1.98 Å20 Å2
3---1.51 Å2
Refinement stepCycle: final / Resolution: 2.58→93.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8164 0 7 55 8226
Biso mean--81.72 52.24 -
Num. residues----1042
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.028294
X-RAY DIFFRACTIONr_bond_other_d0.0020.027855
X-RAY DIFFRACTIONr_angle_refined_deg1.1381.97711158
X-RAY DIFFRACTIONr_angle_other_deg0.812318395
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.96851037
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.64226.556360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.147151559
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2721518
X-RAY DIFFRACTIONr_chiral_restr0.0730.21269
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.029054
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021456
Refine LS restraints NCS

Ens-ID: 1 / Number: 29422 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.58→2.647 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 147 -
Rwork0.35 2819 -
all-2966 -
obs--98.37 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.5111-3.36632.65453.443-2.40882.33920.3240.1983-0.3305-0.3118-0.12330.32060.39850.1234-0.20070.153-0.0566-0.04690.13020.02420.1143-50.773938.645-16.0431
24.4909-3.41281.65993.3685-1.49590.9993-0.04470.10750.60360.0974-0.1304-0.479-0.20780.12170.1750.1195-0.0246-0.00370.045-0.0160.123341.440724.154138.7327
310.8109-2.66624.30593.0838-2.22557.0663-0.7154-0.68270.6480.67810.3074-0.4302-0.81070.01440.4080.23120.0626-0.13440.210.00520.15092.492511.33314.1075
412.219-4.36984.83672.9977-2.86363.48140.17741.0848-0.0651-0.4493-0.15310.21630.11310.0988-0.02430.32930.048-0.12990.50670.08890.3366-10.639552.51626.7409
59.271-3.36972.24923.6633-0.55652.480.48950.4652-0.4953-0.5433-0.19730.3040.3653-0.4099-0.29230.1742-0.0276-0.1390.1834-0.00830.1433.9089-3.384934.6449
69.1062-1.43144.73613.278-2.20387.6432-0.4786-0.08181.12770.2316-0.2995-0.4807-0.3670.78710.77810.1129-0.0953-0.18260.23290.09660.3737-44.074966.4517-10.9301
74.22360.86312.53784.7276-4.77999.9580.1822-0.4525-1.40610.1585-0.9256-1.46421.03661.72150.74340.70820.3361-0.14070.75170.48571.02664.8619-19.237155.5385
87.2944-0.0634-1.25334.70220.6943.5587-0.77570.66823.7724-0.31550.5971.1498-0.926-0.96670.17860.5220.058-0.69580.66360.24042.4397-78.006881.0872-26.1019
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 257
2X-RAY DIFFRACTION2B2 - 257
3X-RAY DIFFRACTION3A258 - 345
4X-RAY DIFFRACTION4B258 - 345
5X-RAY DIFFRACTION5A346 - 436
6X-RAY DIFFRACTION6B346 - 436
7X-RAY DIFFRACTION7A437 - 526
8X-RAY DIFFRACTION8B437 - 525

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